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With the Gene expression ColleCtion you Can:

• Analyzeandannotategeneexpression

experiments

• UseBioConductortoolswithoutprogramming

inR,thewell-knownpublicdomainpackage

forstatisticalcomputingandgraphicsonwhich

BioConducterisbased

• Easilycreateprotocolstocomparedifferent

analysismethods

• IntegrateR/BioConductoranalyseswithanalyses

conductedwithotherPipelinePilotCollections,

includingtheRStatisticsandTextAnalytics

Collections

• Createcomprehensivereportscontaining

elementsfrombothRgraphicsandthe

ReportingCollection

Gene expression ColleCtion

the Gene expression Collection allows you to process, analyze, visualize, annotate, and report

on gene expression experiments, including the individual target genes. Core functionality is

based on BioConductor—the open source and open development software project for the analysis

and comprehension of genomic data. By harnessing the graphical protocol building capabilities

of Pipeline Pilot, the Gene Expression Collection allows you to construct complex BioConductor-

based workflows without writing code, while also making it easy for you to couple Gene Expression

analysis with other Pipeline Pilot-based processes, such as sequence analysis and reporting.

DATASHEET: PiPElinE PiloT

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DS-9035-0811

experiment readers

Affymetrix®andAgilentexperimentscanbereadandprocessed

usingseveralBioConductorpackages(affy,affyPLM,plier,limma).

Processingincludesbackgroundcorrection,normalization,

andsummarization.Excelexperimentreaderscanimportdata

directlyfromexistingspreadsheets.GEOandSOFTreadersenable

processingofdatafromNCBI’sGeneExpressionOmnibus.

experiment analysis

Foldchangeandpairwisedifferentialexpressionarequickly

calculatedforfullexperimentsusingStudent’st-testorWilcoxon

testswithoptionalcontrolformultiplecomparisons.Gene

subsetscanbedefinedbasedoncalculationsorannotations—all

withoutcopyingorcloningdata.Subsetscanalsobedefined

usinggenericcomponentslikeOutlierFilterorTopNFilter.Set

operations(e.g.,union,intersection,andsubtraction)canbe

performedonexistingsubsets.Clusteringcomponents,including

hierarchicalandk-means,arealsoprovided.

data manipulators

Geneexpressionexperimentscanbequitelarge.Onceasubset

ofinterestinggeneshasbeenidentified,theirrelevantportions

oftheexperimentcanberemovedfromtheexperimentrecord,

greatlyspeedingupdownstreamprocessing.Additionally,

individualgenescanbeextracted,leadingtoeasyintegration

withtheSequenceAnalysisCollection.

results annotators

Annotations(e.g.,descriptions,pathwayidentifiers,Gene

Ontologyterms)canbeaddedusingvendor-provideddatavia

BioConductor’sannaffypackage.Inaddition,annotationscanbe

importedfromexistingflatfiles.

VieWers and reportinG tools

UseBioConductorgraphicsorcreateyourowngraphicsand

reportsusingPipelinePilot’sReportingCollection.While

BioConductorprovidessophisticatedplotsandcharts,theycan

bedifficulttoconfigureanduse.TheGeneExpressionCollection

makesiteasytousethesestandardBioConductorreporting

capabilities,whilealsogivingyoutheoptiontoimplement

additionaldataviewsusingtheReportingCollection.Thisgives

youmorecontroloverdisplayfeatures,includinghyperlinksand

tooltips.Suppliedcomponentsincludeheatmaps,annotated

tables,andparallelcoordinateplots.

inteGration With other pipeline pilot ColleCtions

ThecomponentsintheGeneExpressionCollectionaredesigned

toworkseamlesslywithcomponentsfromexistingcollections,

includingtheSequenceAnalysis,RStatistics,DataModeling,and

Chemistry(viapathways)Collections.

TolearnmoreaboutPipelinePilot,goto

accelrys.com/pipeline-pilot